Photos

Abstract

Does Greater Phylogenetic Distance Affect Competition Outcomes in Fungal Communities?

Annette Lewis, Kendall Holcomb, Bárbara Suassuna Schincariol, Josh Stubbs, Geoffery Zahn PhD

Fungi play a critical role in decomposition, affecting nutrient cycling at a global scale. Saprotrophic fungi competitively decompose dead organic matter. However, the role of phylogenetic relatedness on interspecific competition in fungal communities has not received much attention. The theory of phylogenetic over-dispersion suggests that species within a community tend to be less related than expected by chance, therefore limiting competition due to functional redundancy. Similarly, Darwin’s naturalization hypothesis suggests that taxonomically distinct invaders might experience reduced competition and resistance. In this study, we chose three different saprotrophic fungal species with varying relatedness: Aspergillus niger and Fusarium keratoplasticum (from the same family), and Pleurotus ostreatus (from a different phylum). These species were chosen based on decomposition abilities and phylogenetic distances. These species were cultured and placed in seven combinations to assess their ability to decompose and compete as individual fungal populations and as combined communities (e.g., A, B, A+B, B+C, and A+B+C). Each species was placed near a sterilized piece of paper such that competition was evaluated by analyzing the paper coverage in Petri dishes over three weeks. Each Petri dish was analyzed individually based on the average percentage of paper covered and, within combined communities, the percentage of paper each species covered. Interactions between each species and the percentage of the paper covered was recorded for further analysis. Assessing paper coverage allows for the observation of any potential competitive inhibition of decomposition. We hypothesize that decomposing and competitive abilities would be the strongest with A. niger. Despite the fast growth rate of A. niger individually, preliminary results suggest that it was outcompeted when paired with other species. This research highlights the potential nuances in fungal community interactions influenced by phylogenetic relationships, shedding light on the principles of phylogenetic overdispersion and Darwin’s naturalization hypothesis.

Methods

We used three saprophytic fungal species Aspergillus niger, Fusarium keratoplasticum, and Pleurotus ostreatus. A. niger and F. keratoplasticum will be purchased from ATCC.org as freeze-dried and frozen samples. P. ostreatus was already available from Dr. Zahn’s laboratory. These fungal species will then be cultured in Petri dishes.

The cultured fungal samples will be placed in 7 combinations to test their ability to decompose as individual fungi populations and combined communities. For each of the combinations, there will be six replicates.

The sterilized paper’s dimensions are: 1in by 1in

Alongside our results, we will obtain genetic information based on the ITS1 gene in GenBank and construct a phylogenetic tree. We will calculate the phylogenetic relatedness of our species via branch length distance, using ape 5.0 in R. This portion of the research will be conducted to observe species’ phylogenetic diversity and decomposition abilities.

Phylogenetic tree

Initial phylogenetic tree setup. The sequences were obtained from the NCBI, based on the ITS region, and aligned using the EMBL-EBI’s Multiple Sequence Alignment tool, MUSCLE. This tree has no outgroup selected and serves to show the most basic form of this tree.

Phylogenetic tree rooted on Pericharax heteroraphis, a sea sponge, including species names.

Combinations

The different combinations we plan to test:

Species Combination
Aspergillus niger A
Fusarium keratoplasticum B
Pleurotus ostreatus C
Aspergillus niger and Fusarium keratoplasticum A+B
Aspergillus niger and Pleurotus ostreatus A+C
Fusarium keratoplasticum and Pleurotus ostreatus B+C
Aspergillus niger, Fusarium keratoplasticum, and Pleurotus ostreatus A+B+C

Branch lengths

Main. Compute branch lengths based on our sea sponge, Pleurotus ostreatus. In this, the branch lengths associated with the outgroup are excluded here after using it to root the tree.

Species Combination Branch_Length
Aspergillus niger A 0.4614971
Fusarium keratoplasticum B 0.3054016
Pleurotus ostreatus C 0.1341214
Aspergillus niger, Fusarium keratoplasticum A+B 0.5587292
Aspergillus niger, Pleurotus ostreatus A+C 0.5956185
Fusarium keratoplasticum, Pleurotus ostreatus B+C 0.4395229
Aspergillus niger, Fusarium keratoplasticum, Pleurotus ostreatus A+B+C 0.7969353 
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.1341  0.3725  0.4615  0.4703  0.5772  0.7969
## [1] 0.2126998


General. Below shows the general branch length values where the outgroup’s branch length is kept in the final calculation.

Species Combination Branch_Length
Aspergillus niger A 0.6451528
Fusarium keratoplasticum B 0.4890572
Pleurotus ostreatus C 0.3177770
Aspergillus niger, Fusarium keratoplasticum A+B 0.8464696
Aspergillus niger, Pleurotus ostreatus A+C 0.7792742
Fusarium keratoplasticum, Pleurotus ostreatus B+C 0.6231786
Aspergillus niger, Fusarium keratoplasticum, Pleurotus ostreatus A+B+C 0.9805910 
##    Min. 1st Qu.  Median    Mean 3rd Qu.    Max. 
##  0.3178  0.5561  0.6452  0.6688  0.8129  0.9806
## [1] 0.2232897

Our plan will be to stick with this one as the branch lengths here have a slightly larger standard deviation, but this difference is negligible

Experimental results

Line plot

Individual species coverage

Alphabetical

Bond Length

Total combination coverage

Alphabetical

Bond Length

Additional information

Alphabet

Bond length

Scatterplot showing that there seems to be no relationship with total coverage:

## 
## Call:
## lm(formula = total_coverage ~ branch_length + combinations, data = data)
## 
## Residuals:
##    Min     1Q Median     3Q    Max 
## -74.83 -45.77  25.17  32.04  54.23 
## 
## Coefficients: (1 not defined because of singularities)
##                   Estimate Std. Error t value Pr(>|t|)    
## (Intercept)        65.9607     7.7544   8.506  < 2e-16 ***
## branch_length       6.2863    10.6388   0.591 0.554865    
## combinationsB     -23.2642     6.3400  -3.669 0.000269 ***
## combinationsB+C     0.7051     6.1131   0.115 0.908214    
## combinationsA       4.8170     6.1070   0.789 0.430621    
## combinationsA+C   -10.0261     6.2617  -1.601 0.109971    
## combinationsA+B   -20.9485     6.4574  -3.244 0.001258 ** 
## combinationsA+B+C       NA         NA      NA       NA    
## ---
## Signif. codes:  0 '***' 0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1
## 
## Residual standard error: 42.31 on 497 degrees of freedom
## Multiple R-squared:  0.05845,    Adjusted R-squared:  0.04708 
## F-statistic: 5.142 on 6 and 497 DF,  p-value: 3.841e-05

## # Indices of model performance
## 
## AIC      |     AICc |      BIC |    R2 | R2 (adj.) |   RMSE |  Sigma
## --------------------------------------------------------------------
## 5214.207 | 5214.498 | 5247.987 | 0.058 |     0.047 | 42.014 | 42.309